Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• RNA splicing is crucial for eukaryotic gene expression, occurring during or after transcription.
• Understanding the kinetics of transcription-coupled splicing is vital for comprehending gene regulation.
• Budding yeast serves as a model organism for studying fundamental cellular processes like RNA processing.

Purpose of the Study:

• To compare and review next-generation sequencing (NGS) methods for simultaneously quantifying transcription and splicing in yeast.
• To determine the kinetics of RNA splicing relative to transcription for various yeast transcripts.
• To investigate the prevalence of cotranscriptional splicing and identify transcripts with post-transcriptional splicing patterns.

Main Methods:

• Comparative analysis of independent NGS techniques.
• Joint quantification of nascent RNA transcription and pre-messenger RNA splicing.
• Analysis of splicing kinetics in Saccharomyces cerevisiae.

Main Results:

• Splicing is rapid for many yeast transcripts, occurring within seconds of intron transcription and close to the RNA polymerase II.
• Ribosomal protein transcripts exhibit particularly fast and cotranscriptional splicing.
• Some transcripts are spliced inefficiently or primarily post-transcriptionally, suggesting diverse regulatory strategies.
• Evidence suggests intron-mediated gene regulation can be cotranscriptional.

Conclusions:

• Splicing kinetics vary significantly among yeast transcripts, with a substantial portion occurring cotranscriptionally.
• The study highlights the importance of considering splicing intermediates for a complete understanding of splicing dynamics.
• Future research should focus on capturing splicing intermediates to elucidate splicing kinetics and regulation more comprehensively.